Mon 24 Dec 00:36:01 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2pgc-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pgc-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pgc-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pgc-3.2-parrot-mrncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pgc-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pgc-3.2-parrot-mrncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 00:36:05 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pgc-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pgc-3.2-parrot-mrncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 788 and 0 Target number of residues in the AU: 788 Target solvent content: 0.6348 Checking the provided sequence file Detected sequence length: 207 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 5 Adjusted target number of residues: 1035 Adjusted target solvent content: 0.52 Input MTZ file: 2pgc-3.2-parrot-mrncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 18 Cell parameters: 137.477 139.862 60.737 90.000 90.000 90.000 Input sequence file: 2pgc-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 8280 target number of atoms Had to go as low as 0.75 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 98.043 3.200 Wilson plot Bfac: 69.11 19941 reflections ( 99.69 % complete ) and 0 restraints for refining 9222 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.3198 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2893 (Rfree = 0.000) for 9222 atoms. Found 82 (82 requested) and removed 58 (41 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.27 3.18 Search for helices and strands: 0 residues in 0 chains, 9442 seeds are put forward NCS extension: 0 residues added, 9442 seeds are put forward Round 1: 528 peptides, 80 chains. Longest chain 16 peptides. Score 0.476 Round 2: 648 peptides, 77 chains. Longest chain 27 peptides. Score 0.624 Round 3: 680 peptides, 76 chains. Longest chain 30 peptides. Score 0.659 Round 4: 721 peptides, 69 chains. Longest chain 39 peptides. Score 0.719 Round 5: 695 peptides, 68 chains. Longest chain 38 peptides. Score 0.703 Taking the results from Round 4 Chains 79, Residues 652, Estimated correctness of the model 69.1 % 9 chains (157 residues) have been docked in sequence Building loops using Loopy2018 79 chains (652 residues) following loop building 9 chains (157 residues) in sequence following loop building ------------------------------------------------------ 19941 reflections ( 99.69 % complete ) and 14670 restraints for refining 7557 atoms. 11513 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2742 (Rfree = 0.000) for 7557 atoms. Found 67 (67 requested) and removed 66 (33 requested) atoms. Cycle 2: After refmac, R = 0.2632 (Rfree = 0.000) for 7430 atoms. Found 38 (66 requested) and removed 46 (33 requested) atoms. Cycle 3: After refmac, R = 0.2519 (Rfree = 0.000) for 7369 atoms. Found 26 (63 requested) and removed 39 (33 requested) atoms. Cycle 4: After refmac, R = 0.2442 (Rfree = 0.000) for 7331 atoms. Found 28 (62 requested) and removed 41 (33 requested) atoms. Cycle 5: After refmac, R = 0.2349 (Rfree = 0.000) for 7291 atoms. Found 24 (60 requested) and removed 36 (32 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.29 3.20 Search for helices and strands: 0 residues in 0 chains, 7547 seeds are put forward NCS extension: 31 residues added (3 deleted due to clashes), 7578 seeds are put forward Round 1: 653 peptides, 78 chains. Longest chain 26 peptides. Score 0.625 Round 2: 701 peptides, 66 chains. Longest chain 39 peptides. Score 0.715 Round 3: 702 peptides, 63 chains. Longest chain 43 peptides. Score 0.727 Round 4: 738 peptides, 64 chains. Longest chain 39 peptides. Score 0.749 Round 5: 727 peptides, 71 chains. Longest chain 43 peptides. Score 0.717 Taking the results from Round 4 Chains 70, Residues 674, Estimated correctness of the model 74.9 % 10 chains (177 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 173 D and 179 D 68 chains (678 residues) following loop building 9 chains (182 residues) in sequence following loop building ------------------------------------------------------ 19941 reflections ( 99.69 % complete ) and 14450 restraints for refining 7560 atoms. 11139 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2612 (Rfree = 0.000) for 7560 atoms. Found 44 (60 requested) and removed 54 (33 requested) atoms. Cycle 7: After refmac, R = 0.2466 (Rfree = 0.000) for 7513 atoms. Found 18 (59 requested) and removed 41 (33 requested) atoms. Cycle 8: After refmac, R = 0.2356 (Rfree = 0.000) for 7471 atoms. Found 24 (58 requested) and removed 42 (33 requested) atoms. Cycle 9: After refmac, R = 0.2259 (Rfree = 0.000) for 7433 atoms. Found 16 (55 requested) and removed 38 (33 requested) atoms. Cycle 10: After refmac, R = 0.2140 (Rfree = 0.000) for 7398 atoms. Found 17 (54 requested) and removed 35 (33 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.26 3.17 Search for helices and strands: 0 residues in 0 chains, 7634 seeds are put forward NCS extension: 66 residues added (9 deleted due to clashes), 7700 seeds are put forward Round 1: 649 peptides, 76 chains. Longest chain 28 peptides. Score 0.630 Round 2: 694 peptides, 69 chains. Longest chain 41 peptides. Score 0.698 Round 3: 691 peptides, 68 chains. Longest chain 30 peptides. Score 0.700 Round 4: 706 peptides, 67 chains. Longest chain 36 peptides. Score 0.715 Round 5: 694 peptides, 65 chains. Longest chain 44 peptides. Score 0.713 Taking the results from Round 4 Chains 75, Residues 639, Estimated correctness of the model 68.3 % 11 chains (197 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 173 B and 184 B 73 chains (647 residues) following loop building 10 chains (207 residues) in sequence following loop building ------------------------------------------------------ 19941 reflections ( 99.69 % complete ) and 13981 restraints for refining 7559 atoms. 10645 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2537 (Rfree = 0.000) for 7559 atoms. Found 46 (54 requested) and removed 53 (33 requested) atoms. Cycle 12: After refmac, R = 0.2406 (Rfree = 0.000) for 7527 atoms. Found 26 (52 requested) and removed 42 (33 requested) atoms. Cycle 13: After refmac, R = 0.2277 (Rfree = 0.000) for 7501 atoms. Found 19 (51 requested) and removed 37 (33 requested) atoms. Cycle 14: After refmac, R = 0.2193 (Rfree = 0.000) for 7476 atoms. Found 12 (50 requested) and removed 34 (33 requested) atoms. Cycle 15: After refmac, R = 0.2153 (Rfree = 0.000) for 7443 atoms. Found 19 (48 requested) and removed 33 (33 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.25 3.16 Search for helices and strands: 0 residues in 0 chains, 7681 seeds are put forward NCS extension: 12 residues added (12 deleted due to clashes), 7693 seeds are put forward Round 1: 654 peptides, 81 chains. Longest chain 30 peptides. Score 0.612 Round 2: 688 peptides, 69 chains. Longest chain 37 peptides. Score 0.693 Round 3: 663 peptides, 66 chains. Longest chain 39 peptides. Score 0.684 Round 4: 687 peptides, 64 chains. Longest chain 37 peptides. Score 0.712 Round 5: 693 peptides, 69 chains. Longest chain 28 peptides. Score 0.697 Taking the results from Round 4 Chains 66, Residues 623, Estimated correctness of the model 67.7 % 6 chains (119 residues) have been docked in sequence Building loops using Loopy2018 66 chains (623 residues) following loop building 6 chains (119 residues) in sequence following loop building ------------------------------------------------------ 19941 reflections ( 99.69 % complete ) and 15242 restraints for refining 7559 atoms. 12377 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2497 (Rfree = 0.000) for 7559 atoms. Found 31 (47 requested) and removed 49 (33 requested) atoms. Cycle 17: After refmac, R = 0.2418 (Rfree = 0.000) for 7517 atoms. Found 16 (46 requested) and removed 39 (33 requested) atoms. Cycle 18: After refmac, R = 0.2663 (Rfree = 0.000) for 7477 atoms. Found 44 (44 requested) and removed 48 (33 requested) atoms. Cycle 19: After refmac, R = 0.2561 (Rfree = 0.000) for 7455 atoms. Found 43 (43 requested) and removed 44 (33 requested) atoms. Cycle 20: After refmac, R = 0.2184 (Rfree = 0.000) for 7444 atoms. Found 19 (41 requested) and removed 34 (33 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.31 3.22 Search for helices and strands: 0 residues in 0 chains, 7672 seeds are put forward NCS extension: 11 residues added (5 deleted due to clashes), 7683 seeds are put forward Round 1: 631 peptides, 78 chains. Longest chain 28 peptides. Score 0.603 Round 2: 661 peptides, 67 chains. Longest chain 39 peptides. Score 0.679 Round 3: 661 peptides, 71 chains. Longest chain 35 peptides. Score 0.662 Round 4: 666 peptides, 66 chains. Longest chain 39 peptides. Score 0.687 Round 5: 650 peptides, 63 chains. Longest chain 37 peptides. Score 0.685 Taking the results from Round 4 Chains 72, Residues 600, Estimated correctness of the model 62.4 % 7 chains (136 residues) have been docked in sequence ------------------------------------------------------ 19941 reflections ( 99.69 % complete ) and 15256 restraints for refining 7560 atoms. 12410 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2440 (Rfree = 0.000) for 7560 atoms. Found 33 (40 requested) and removed 58 (33 requested) atoms. Cycle 22: After refmac, R = 0.2305 (Rfree = 0.000) for 7512 atoms. Found 28 (40 requested) and removed 34 (33 requested) atoms. Cycle 23: After refmac, R = 0.2269 (Rfree = 0.000) for 7499 atoms. Found 22 (40 requested) and removed 39 (33 requested) atoms. Cycle 24: After refmac, R = 0.2246 (Rfree = 0.000) for 7474 atoms. Found 25 (40 requested) and removed 37 (33 requested) atoms. Cycle 25: After refmac, R = 0.2211 (Rfree = 0.000) for 7451 atoms. Found 30 (40 requested) and removed 34 (33 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.30 3.21 Search for helices and strands: 0 residues in 0 chains, 7691 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 7714 seeds are put forward Round 1: 598 peptides, 85 chains. Longest chain 27 peptides. Score 0.533 Round 2: 656 peptides, 70 chains. Longest chain 29 peptides. Score 0.662 Round 3: 660 peptides, 76 chains. Longest chain 28 peptides. Score 0.640 Round 4: 650 peptides, 75 chains. Longest chain 30 peptides. Score 0.635 Round 5: 656 peptides, 71 chains. Longest chain 34 peptides. Score 0.658 Taking the results from Round 2 Chains 72, Residues 586, Estimated correctness of the model 56.7 % 5 chains (101 residues) have been docked in sequence ------------------------------------------------------ 19941 reflections ( 99.69 % complete ) and 15520 restraints for refining 7560 atoms. 12825 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2355 (Rfree = 0.000) for 7560 atoms. Found 40 (40 requested) and removed 45 (33 requested) atoms. Cycle 27: After refmac, R = 0.2254 (Rfree = 0.000) for 7541 atoms. Found 24 (40 requested) and removed 35 (33 requested) atoms. Cycle 28: After refmac, R = 0.2171 (Rfree = 0.000) for 7520 atoms. Found 28 (40 requested) and removed 34 (33 requested) atoms. Cycle 29: After refmac, R = 0.2098 (Rfree = 0.000) for 7504 atoms. Found 21 (40 requested) and removed 38 (33 requested) atoms. Cycle 30: After refmac, R = 0.2066 (Rfree = 0.000) for 7481 atoms. Found 13 (40 requested) and removed 33 (33 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.32 3.23 Search for helices and strands: 0 residues in 0 chains, 7689 seeds are put forward NCS extension: 12 residues added (8 deleted due to clashes), 7701 seeds are put forward Round 1: 565 peptides, 82 chains. Longest chain 23 peptides. Score 0.510 Round 2: 636 peptides, 78 chains. Longest chain 24 peptides. Score 0.608 Round 3: 620 peptides, 74 chains. Longest chain 24 peptides. Score 0.610 Round 4: 620 peptides, 71 chains. Longest chain 35 peptides. Score 0.624 Round 5: 631 peptides, 73 chains. Longest chain 34 peptides. Score 0.626 Taking the results from Round 5 Chains 76, Residues 558, Estimated correctness of the model 47.9 % 5 chains (91 residues) have been docked in sequence ------------------------------------------------------ 19941 reflections ( 99.69 % complete ) and 15866 restraints for refining 7560 atoms. 13349 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2391 (Rfree = 0.000) for 7560 atoms. Found 40 (40 requested) and removed 44 (33 requested) atoms. Cycle 32: After refmac, R = 0.2285 (Rfree = 0.000) for 7529 atoms. Found 17 (40 requested) and removed 35 (33 requested) atoms. Cycle 33: After refmac, R = 0.2195 (Rfree = 0.000) for 7499 atoms. Found 23 (40 requested) and removed 33 (33 requested) atoms. Cycle 34: After refmac, R = 0.2153 (Rfree = 0.000) for 7478 atoms. Found 11 (40 requested) and removed 34 (33 requested) atoms. Cycle 35: After refmac, R = 0.2107 (Rfree = 0.000) for 7452 atoms. Found 13 (40 requested) and removed 33 (33 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.27 3.18 Search for helices and strands: 0 residues in 0 chains, 7656 seeds are put forward NCS extension: 43 residues added (9 deleted due to clashes), 7699 seeds are put forward Round 1: 557 peptides, 74 chains. Longest chain 21 peptides. Score 0.543 Round 2: 608 peptides, 70 chains. Longest chain 31 peptides. Score 0.617 Round 3: 606 peptides, 70 chains. Longest chain 26 peptides. Score 0.615 Round 4: 599 peptides, 66 chains. Longest chain 27 peptides. Score 0.626 Round 5: 611 peptides, 68 chains. Longest chain 31 peptides. Score 0.629 Taking the results from Round 5 Chains 71, Residues 543, Estimated correctness of the model 48.6 % 6 chains (78 residues) have been docked in sequence ------------------------------------------------------ 19941 reflections ( 99.69 % complete ) and 16015 restraints for refining 7560 atoms. 13617 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2445 (Rfree = 0.000) for 7560 atoms. Found 40 (40 requested) and removed 38 (33 requested) atoms. Cycle 37: After refmac, R = 0.2363 (Rfree = 0.000) for 7551 atoms. Found 36 (40 requested) and removed 34 (33 requested) atoms. Cycle 38: After refmac, R = 0.2244 (Rfree = 0.000) for 7542 atoms. Found 27 (40 requested) and removed 34 (33 requested) atoms. Cycle 39: After refmac, R = 0.2202 (Rfree = 0.000) for 7526 atoms. Found 30 (40 requested) and removed 34 (33 requested) atoms. Cycle 40: After refmac, R = 0.2152 (Rfree = 0.000) for 7511 atoms. Found 34 (40 requested) and removed 33 (33 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 3.22 Search for helices and strands: 0 residues in 0 chains, 7713 seeds are put forward NCS extension: 21 residues added (5 deleted due to clashes), 7734 seeds are put forward Round 1: 514 peptides, 71 chains. Longest chain 17 peptides. Score 0.508 Round 2: 570 peptides, 67 chains. Longest chain 33 peptides. Score 0.592 Round 3: 586 peptides, 70 chains. Longest chain 39 peptides. Score 0.594 Round 4: 588 peptides, 65 chains. Longest chain 31 peptides. Score 0.620 Round 5: 575 peptides, 67 chains. Longest chain 27 peptides. Score 0.597 Taking the results from Round 4 Chains 67, Residues 523, Estimated correctness of the model 46.3 % 6 chains (61 residues) have been docked in sequence ------------------------------------------------------ 19941 reflections ( 99.69 % complete ) and 16206 restraints for refining 7560 atoms. 13926 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2389 (Rfree = 0.000) for 7560 atoms. Found 40 (40 requested) and removed 40 (33 requested) atoms. Cycle 42: After refmac, R = 0.2278 (Rfree = 0.000) for 7545 atoms. Found 40 (40 requested) and removed 34 (33 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2293 (Rfree = 0.000) for 7542 atoms. Found 40 (40 requested) and removed 34 (33 requested) atoms. Cycle 44: After refmac, R = 0.2255 (Rfree = 0.000) for 7544 atoms. Found 29 (40 requested) and removed 37 (33 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.2081 (Rfree = 0.000) for 7528 atoms. Found 20 (40 requested) and removed 33 (33 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.25 3.16 Search for helices and strands: 0 residues in 0 chains, 7709 seeds are put forward NCS extension: 11 residues added (12 deleted due to clashes), 7720 seeds are put forward Round 1: 451 peptides, 67 chains. Longest chain 22 peptides. Score 0.451 Round 2: 508 peptides, 67 chains. Longest chain 22 peptides. Score 0.522 Round 3: 507 peptides, 63 chains. Longest chain 24 peptides. Score 0.542 Round 4: 500 peptides, 61 chains. Longest chain 22 peptides. Score 0.545 Round 5: 507 peptides, 64 chains. Longest chain 24 peptides. Score 0.537 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 63, Residues 439, Estimated correctness of the model 25.4 % 2 chains (29 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2pgc-3_warpNtrace.pdb as input Building loops using Loopy2018 63 chains (439 residues) following loop building 2 chains (29 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 19941 reflections ( 99.69 % complete ) and 17081 restraints for refining 7558 atoms. 15273 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2282 (Rfree = 0.000) for 7558 atoms. Found 0 (40 requested) and removed 33 (33 requested) atoms. Cycle 47: After refmac, R = 0.2146 (Rfree = 0.000) for 7519 atoms. Found 0 (40 requested) and removed 33 (33 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2163 (Rfree = 0.000) for 7474 atoms. Found 0 (40 requested) and removed 33 (33 requested) atoms. Cycle 49: After refmac, R = 0.2087 (Rfree = 0.000) for 7431 atoms. TimeTaking 82.6